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Journal club on Sep-17-2010

I suggest we read a paper recently published in Science. The title is “Genetic Reactivation of Cone Photoreceptors Restores Visual Responses in Retinitis Pigmentosa”. Retinal pigmentosa is so far found to be caused by diverse mutations in 44 genes. Patients with this diease will irreversibly lose their vision, as rod photoreceptors will die early and cone photoreceptor will be light-insensitive owing to the morphological change. But normally cone photoreceptors could persist longer. In this study, the authers genetically targeted a light activated chloride pump, which is one of the candidates for reactivating vertebrate photoreceptors, into the photorecepors of mouse models of retinitis pigmentosa by means of adneo-associated viruses, and successfully restored their light sensitivity. They also found the protein could reactivate the light-insensitive human photoreceptors in ex vivo retinas. Is this a good news for people who suffer from retinitis pigmentosa and blindness? Let’s find out together.

Link to the paper:

http://www.sciencemag.org/cgi/content/full/329/5990/413

2010-08-29 New articles we read this week

Ethics

  1. Coors ME, Glover JJ, Juengst ET, Sikela JM. The ethics of using transgenic non-human primates to study what makes us human. Nat Rev Genet. 2010 Sep;11(9):658-62. PubMed PMID: 20717156.

Systems biology

  1. Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP. Computational solutions to large-scale data management and analysis. Nat Rev Genet. 2010 Sep;11(9):647-57. PubMed PMID: 20717155.
  2. Morelli LG, Ares S, Herrgen L, Schröter C, Jülicher F, Oates AC. Delayed coupling theory of vertebrate segmentation. HFSP J. 2009;3(1):55-66. Epub 2008 Dec 10.

Evolution

  1. Klingenberg CP. Evolution and development of shape: integrating quantitative approaches. Nat Rev Genet. 2010 Sep;11(9):623-35. Epub 2010 Aug 10. PubMed PMID: 20697423.
  2. Cockburn A. Evolutionary biology: Oh sibling, who art thou? Nature. 2010 Aug 19;466(7309):930-1. PubMed PMID: 20725030.
  3. Cornwallis CK, West SA, Davis KE, Griffin AS. Promiscuity and the evolutionary transition to complex societies. Nature. 2010 Aug 19;466(7309):969-72. PubMed PMID: 20725039.

Aging and neuroscience

  1. Valdez G, Tapia JC, Kang H, Clemenson GD Jr, Gage FH, Lichtman JW, Sanes JR. Attenuation of age-related changes in mouse neuromuscular synapses by caloric restriction and exercise. Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14863-8. Epub 2010 Aug 2. PubMed PMID: 20679195.

Genomics, Genetics

  1. Hutt D, Balch WE. Cell Biology. The proteome in balance. Science. 2010 Aug 13;329(5993):766-7. PubMed PMID: 20705837.
  2. Gregg C, Zhang J, Weissbourd B, Luo S, Schroth GP, Haig D, Dulac C. High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science. 2010 Aug 6;329(5992):643-8. Epub 2010 Jul 8. PubMed PMID:20616232.
  3. Gregg C, Zhang J, Butler JE, Haig D, Dulac C. Sex-specific parent-of-origin allelic expression in the mouse brain. Science. 2010 Aug 6;329(5992):682-5. Epub 2010 Jul 8. PubMed PMID: 20616234.

2010-08-22 new articles we read this week

Genetics

  1. Klein RJ, Xu X, Mukherjee S, Willis J, Hayes J. Successes of Genome-wide Association Studies. Cell. 2010 Aug 6;142(3):350-1. PubMed PMID: 20691890.
  2. Wang K, Bucan M, Grant SF, Schellenberg G, Hakonarson H. Strategies for genetic studies of complex diseases. Cell. 2010 Aug 6;142(3):351-3. PubMed PMID: 20691891.
  3. McClellan J, King MC. Response: why it is time to sequence. Cell. 2010 Aug 6;142(3):353-5. PubMed PMID: 20691892.
  4. Wilkinson LS. Developmental biology. Which parental gene gets the upper hand? Science. 2010 Aug 6;329(5992):636-7. PubMed PMID: 20689006.

Segmentation

  1. Masamizu Y, Ohtsuka T, Takashima Y, Nagahara H, Takenaka Y, Yoshikawa K, Okamura H, Kageyama R. Real-time imaging of the somite segmentation clock: revelation of unstable oscillators in the individual presomitic mesoderm cells. Proc Natl Acad Sci U S A. 2006 Jan 31;103(5):1313-8. Epub 2006 Jan 23. PubMed PMID: 16432209; PubMed Central PMCID: PMC1345707.
  2. Hirata H, Bessho Y, Kokubu H, Masamizu Y, Yamada S, Lewis J, Kageyama R. Instability of Hes7 protein is crucial for the somite segmentation clock. Nat Genet. 2004 Jul;36(7):750-4. Epub 2004 May 30. PubMed PMID: 15170214.

Delta-Notch

  1. Sang L, Coller HA, Roberts JM. Control of the reversibility of cellular quiescence by the transcriptional repressor HES1. Science. 2008 Aug 22;321(5892):1095-100. PubMed PMID: 18719287; PubMed Central PMCID: PMC2721335.
  2. Breunig JJ, Silbereis J, Vaccarino FM, Sestan N, Rakic P. Notch regulates cell fate and dendrite morphology of newborn neurons in the postnatal dentate gyrus. Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20558-63. Epub 2007 Dec 11. PubMed PMID: 18077357; PubMed Central PMCID: PMC2154470.
  3. Baek JH, Hatakeyama J, Sakamoto S, Ohtsuka T, Kageyama R. Persistent and high levels of Hes1 expression regulate boundary formation in the developing central nervous system. Development. 2006 Jul;133(13):2467-76. Epub 2006 May 25. PubMed PMID: 16728479.
  4. Hirata H, Yoshiura S, Ohtsuka T, Bessho Y, Harada T, Yoshikawa K, Kageyama R. Oscillatory expression of the bHLH factor Hes1 regulated by a negative feedback loop. Science. 2002 Oct 25;298(5594):840-3. PubMed PMID: 12399594.

Systems Biology

  1. Rusk N. Advent of synthetic life. Nat Methods. 2010 Jul;7(7):487. PubMed PMID: 20603906.
  2. Moseley JB, Nurse P. Cell division intersects with cell geometry. Cell. 2010 Jul 23;142(2):184-8. PubMed PMID: 20655459.

Neuroscience

  1. Clark DA, de Vries SE, Clandinin TR. Watching the fly brain in action. Nat Methods. 2010 Jul;7(7):505-6. PubMed PMID: 20588268.

Nature Insights Plasticity

  1. Yamanaka S, Blau HM. Nuclear reprogramming to a pluripotent state by three approaches. Nature. 2010 Jun 10;465(7299):704-12. Review. PubMed PMID: 20535199; PubMed Central PMCID:PMC2901154.
  2. Pera MF, Tam PP. Extrinsic regulation of pluripotent stem cells. Nature. 2010 Jun 10;465(7299):713-20. Review. PubMed PMID: 20535200.
  3. Petronis A. Epigenetics as a unifying principle in the aetiology of complex traits and diseases. Nature. 2010 Jun 10;465(7299):721-7. PubMed PMID: 20535201.
  4. Dulac C. Brain function and chromatin plasticity. Nature. 2010 Jun
    10;465(7299):728-35. Review. PubMed PMID: 20535202.
  5. Spiller DG, Wood CD, Rand DA, White MR. Measurement of single-cell dynamics. Nature. 2010 Jun 10;465(7299):736-45. Review. PubMed PMID: 20535203.

2010-08-16 new articles we read this week

  1. Corbo JC, Lawrence KA, Karlstetter M, Myers CA, Abdelaziz M, Dirkes W, Weigelt K, Seifert M, Benes V, Fritsche LG, Weber BH, Langmann T. CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors. Genome Res. 2010 Aug 6. [Epub ahead of print] PubMed PMID: 20693478.
  2. Holmes Finch. Comparison of Distance Measures in Cluster Analysis with Dichotomous Data.[pdf]
  3. Grimm O, Wieschaus E. The Bicoid gradient is shaped independently of nuclei. Development. 2010 Sep;137(17):2857-62. PubMed PMID: 20699297.
  4. Cepko C. Neuroscience. Seeing the light of day. Science. 2010 Jul 23;329(5990):403-4. PubMed PMID: 20651144.
  5. Greenbury SF, Johnston IG, Smith MA, Doye JP, Louis AA. The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks. J Theor Biol. 2010 Aug 6. [Epub ahead of print] PubMed PMID: 20696172.

Is My Thesis Hot or Not?

It has been a while since the last update… well, just come across a funny website which can be useful in some ways.

Is My Thesis Hot or Not?

By reading a number of titles from other people’s work, you will start to appreciate what works in your own setting and what does not.

Most people are not observant

This is not a new idea, but look at this funny experiment done at Harvard. I just can’t stop wondering how much we are missing when we are staring at our experiments with our own preconception…


Most People Are Not Observant – Watch more Funny Videos

Christmas party etc.

Please share/finalize your ideas for

  1. party location
  2. gift exchange
  3. lab present

Why Roosters Have Wattles?

From Smithsonian.com

The test hens responded more quickly to the tidbitting males that had the normal or stationary wattles, less quickly to the one with the extra floppy wattle (….) and slowest to the male lacking wattles. After the hen’s attention was gained, though, she reacted about the same to each of the four animated chickens. Smith suggests that the wattle helps a rooster gain a hen’s attention when he is tidbitting, rather like a human guy wearing flashy clothes while doing his best dance moves to try and pick up chicks.

The Nobel Prize in Physiology or Medicine 2009

goes to Elizabeth H. Blackburn, Carol W. Greider, Jack W. Szostak.

“for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase”

link to Nobel prize.org

link to the press release

2009 Ig Nobel prize winners!!!

Some interesting work here, the full winner list is available from their website:

PEACE PRIZE

Stephan Bolliger, Steffen Ross, Lars Oesterhelweg, Michael Thali and Beat Kneubuehl of the University of Bern, Switzerland, for determining — by experiment — whether it is better to be smashed over the head with a full bottle of beer or with an empty bottle.
REFERENCE: “Are Full or Empty Beer Bottles Sturdier and Does Their Fracture-Threshold Suffice to Break the Human Skull?” Stephan A. Bolliger, Steffen Ross, Lars Oesterhelweg, Michael J. Thali and Beat P. Kneubuehl, Journal of Forensic and Legal Medicine, vol. 16, no. 3, April 2009, pp. 138-42.

VETERINARY MEDICINE PRIZE

Catherine Douglas and Peter Rowlinson of Newcastle University, Newcastle-Upon-Tyne, UK, for showing that cows who have names give more milk than cows that are nameless.
REFERENCE: “Exploring Stock Managers’ Perceptions of the Human-Animal Relationship on Dairy Farms and an Association with Milk Production,” Catherine Bertenshaw [Douglas] and Peter Rowlinson, Anthrozoos, vol. 22, no. 1, March 2009, pp. 59-69.

ECONOMICS PRIZE

The directors, executives, and auditors of four Icelandic banks — Kaupthing Bank, Landsbanki, Glitnir Bank, and Central Bank of Iceland — for demonstrating that tiny banks can be rapidly transformed into huge banks, and vice versa — and for demonstrating that similar things can be done to an entire national economy.

MEDICINE PRIZE

Donald L. Unger, of Thousand Oaks, California, USA, for investigating a possible cause of arthritis of the fingers, by diligently cracking the knuckles of his left hand — but never cracking the knuckles of his right hand — every day for more than sixty (60) years.
REFERENCE: “Does Knuckle Cracking Lead to Arthritis of the Fingers?”, Donald L. Unger, Arthritis and Rheumatism, vol. 41, no. 5, 1998, pp. 949-50.

LITERATURE PRIZE

Ireland’s police service (An Garda Siochana), for writing and presenting more than fifty traffic tickets to the most frequent driving offender in the country — Prawo Jazdy — whose name in Polish means “Driving License”.

MATHEMATICS PRIZE

Gideon Gono, governor of Zimbabwe’s Reserve Bank, for giving people a simple, everyday way to cope with a wide range of numbers — from very small to very big — by having his bank print bank notes with denominations ranging from one cent ($.01) to one hundred trillion dollars ($100,000,000,000,000).
REFERENCE: Zimbabwe’s Casino Economy — Extraordinary Measures for Extraordinary Challenges, Gideon Gono, ZPH Publishers, Harare, 2008, ISBN 978-079-743-679-4.